To make this more concrete. Consider one of their projects (http://harc.ycr.org/project/), the Block-based programming: what's the evidence that this is a superior way for learning programming? What's the evidence that so-called computational thinking enhances cognitive ability or is transferrable to day-to-day thinking?
Furthermore, much of their computer-based education ideas are based on Seymour Papert's research and ideas which in turn was based on Piaget's theories on mental development. Those theories, however, have been thoroughly challenged and is all but outdated.
EDIT: this was the top comment and actively upvoted, now it seems that the mods have placed it at the end just before comments with negative points. I had heard of YC's sensitivity towards any criticism but this seems extreme. Whats the point discussions without criticism.